# Correlation analysis between plasma circulating tumour deoxyribonucleic acid variations and survival in patients with hepatocellular carcinoma

**Authors:** Songtao Liu, Jingjing Chen, Qiaoxin Wei, Jinhuan Wang, Fang Xiong, Jia Guo, Yang Wang, Mei Liu

PMC · DOI: 10.3389/fonc.2025.1653475 · Frontiers in Oncology · 2026-02-10

## TL;DR

This study shows that plasma tumor DNA levels and specific gene mutations can predict survival in liver cancer patients.

## Contribution

The study identifies LRP1B mutations as a novel prognostic biomarker for hepatocellular carcinoma patients undergoing systemic therapy.

## Key findings

- Tumor mutation burden increases with higher Barcelona Clinic Liver Cancer stages but decreases in stage D.
- Patients with TP53 and LRP1B mutations had shorter survival, with LRP1B mutations significantly reducing survival during systemic therapy.
- Tumor mutation burden and Child–Pugh scores were closely associated with overall survival in hepatocellular carcinoma patients.

## Abstract

This study aimed to analyse the variation of circulating tumour DNA (ctDNA) in patients with hepatocellular carcinoma (HCC).

Newly diagnosed patients with HCC admitted between March 2022 and October 2023 were prospectively enrolled. Plasma ctDNA testing was performed before treatment, and clinical information, treatment regimens and survival data were collected.

A total of 166 patients with HCC were enrolled, including 127 men and 39 women, with a mean age of 58.1±10.0 years. Of these, 137 patients were infected with hepatitis B virus, and 129 had underlying cirrhosis. According to the Barcelona Clinic Liver Cancer (BCLC) staging system, 74, 20, 52 and 20 patients were classified as stages A, B, C and D, respectively. Tumour mutation burden (TMB) ranged from 0 to 35.48 mutations per Mb; it increased with higher BCLC stages but decreased in stage D. The top five mutated genes were TP53 (39.8%), CTNNB1 (15.7%), LRP1B (12.0%), ARID1A (10.8%) and FAT3 (9.0%). Patients with TP53 and LRP1B mutations exhibited shorter survival (p < 0.05). Among the 54 patients who received systemic therapy, only those with LRP1B mutations had significantly reduced overall survival (OS) (p = 0.048). Cox multivariate survival analysis revealed that TMB and Child–Pugh scores were closely associated with OS. Regardless of tumour stage, LRP1B mutation was significantly correlated with OS in patients undergoing systemic therapy.

Circulating tumour DNA testing demonstrated that TMB is closely associated with OS in patients with HCC. Patients with HCC with LRP1B mutations had significantly shorter survival when receiving systemic therapy. Circulating tumour DNA testing holds considerable value in predicting HCC prognosis and may serve as a biomarker for assessing patient outcomes.

## Linked entities

- **Genes:** TP53 (tumor protein p53) [NCBI Gene 7157], CTNNB1 (catenin beta 1) [NCBI Gene 1499], LRP1B (LDL receptor related protein 1B) [NCBI Gene 53353], ARID1A (AT-rich interaction domain 1A) [NCBI Gene 8289], FAT3 (FAT atypical cadherin 3) [NCBI Gene 120114]
- **Diseases:** hepatocellular carcinoma (MONDO:0007256), cirrhosis (MONDO:0005155)

## Full-text entities

- **Genes:** AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, FAT3 (FAT atypical cadherin 3) [NCBI Gene 120114] {aka CDHF15, CDHR10, hFat3}, TERT (telomerase reverse transcriptase) [NCBI Gene 7015] {aka CMM9, DKCA2, DKCB4, EST2, PFBMFT1, TCS1}, AFP (alpha fetoprotein) [NCBI Gene 174] {aka AFPD, FETA, HPAFP}, BCL2 (BCL2 apoptosis regulator) [NCBI Gene 596] {aka Bcl-2, PPP1R50}, RB1 (RB transcriptional corepressor 1) [NCBI Gene 5925] {aka OSRC, PPP1R130, RB, p105-Rb, p110-RB1, pRb}, PTPRT (protein tyrosine phosphatase receptor type T) [NCBI Gene 11122] {aka R-PTP-T, RPTP-rho, RPTPrho}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, FGA (fibrinogen alpha chain) [NCBI Gene 2243] {aka AMYLD2, Fib2}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, NCSTN (nicastrin) [NCBI Gene 23385] {aka ATAG1874}, LRP1B (LDL receptor related protein 1B) [NCBI Gene 53353] {aka LRP-1B, LRP-DIT, LRPDIT}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) [NCBI Gene 5290] {aka CCM4, CLAPO, CLOVE, CWS5, HMH, MCAP}, BRCA2 (BRCA2 DNA repair associated) [NCBI Gene 675] {aka BRCC2, BROVCA2, FACD, FAD, FAD1, FANCD}, FAT1 (FAT atypical cadherin 1) [NCBI Gene 2195] {aka CDHF7, CDHR8, FAT, ME5, hFat1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, MCL1 (MCL1 apoptosis regulator, BCL2 family member) [NCBI Gene 4170] {aka BCL2L3, EAT, MCL1-ES, MCL1L, MCL1S, Mcl-1}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, SPTA1 (spectrin alpha, erythrocytic 1) [NCBI Gene 6708] {aka EL2, HPP, HS3, SPH3, SPTA}, BRCA1 (BRCA1 DNA repair associated) [NCBI Gene 672] {aka BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4}, HHLA2 (HHLA2 member of B7 family) [NCBI Gene 11148] {aka B7-H5, B7-H7, B7H7, B7y}, ARID1A (AT-rich interaction domain 1A) [NCBI Gene 8289] {aka B120, BAF250, BAF250a, BM029, C1orf4, CSS2}, RET (ret proto-oncogene) [NCBI Gene 5979] {aka CDHF12, CDHR16, HSCR1, MEN2A, MEN2B, MTC1}, PNKP (polynucleotide kinase 3'-phosphatase) [NCBI Gene 11284] {aka AOA4, CMT2B2, EIEE10, MCSZ, PNK}, FGFR3 (fibroblast growth factor receptor 3) [NCBI Gene 2261] {aka ACH, CD333, CEK2, HSFGFR3EX, JTK4}
- **Diseases:** liver metastases (MESH:D009362), cirrhosis (MESH:D005355), death (MESH:D003643), immunodeficiency diseases (MESH:D007153), OS (MESH:D011475), infected (MESH:D007239), genomic abnormalities (MESH:D042822), Cancer (MESH:D009369), liver cirrhosis (MESH:D008103), hepatitis B virus (HBV) infection (MESH:D006509), liver dysfunction (MESH:D017093), BCLC stage D (MESH:D006528), necrosis (MESH:D009336)
- **Chemicals:** Lipofectamine 3000 (-), NaCl (MESH:D012965), doxorubicin (MESH:D004317), acid (MESH:D000143), puromycin (MESH:D011691), penicillin (MESH:D010406), NP40 (MESH:C010615), polyacrylamide (MESH:C016679), streptomycin (MESH:D013307), donafenib (MESH:C000710249), sodium azide (MESH:D019810), CO2 (MESH:D002245), sintilimab (MESH:C000632826), atezolizumab (MESH:C000594389), lenvatinib (MESH:C531958), polyvinylidene difluoride (MESH:C024865), alcohol (MESH:D000438), SDS (MESH:D012967), bevacizumab (MESH:D000068258), dimethyl sulfoxide (MESH:D004121), McCoy's 5A medium (MESH:C113109)
- **Species:** Homo sapiens (human, species) [taxon 9606], Hepatitis B virus (no rank) [taxon 10407]
- **Cell lines:** HepG2 — Homo sapiens (Human), Hepatoblastoma, Cancer cell line (CVCL_0027), CL-0103 — Homo sapiens (Human), Transformed cell line (CVCL_K373), L3000-015 — Homo sapiens (Human), Finite cell line (CVCL_A2LW), HCT116 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_0291), P8833 — Atilax paludinosus (Marsh mongoose), Finite cell line (CVCL_6365)

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## References

34 references — full list in the complete paper: https://tomesphere.com/paper/PMC12929130/full.md

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Source: https://tomesphere.com/paper/PMC12929130